ompBAM
This is the development version of ompBAM; for the stable release version, see ompBAM.
C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files
Bioconductor version: Development (3.24)
This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads 'behind the scenes', so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged included within ompBAM.
Author: Alex Chit Hei Wong [aut, cre, cph]
Maintainer: Alex Chit Hei Wong <alexchwong.github at gmail.com>
citation("ompBAM")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ompBAM")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ompBAM")| ompBAM API Documentation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, DataImport, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | utils, Rcpp |
| System Requirements | |
| URL | https://github.com/alexchwong/ompBAM |
| Bug Reports | https://support.bioconductor.org/ |
See More
| Suggests | RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | SpliceWiz |
| Suggests Me | |
| Links To Me | SpliceWiz |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ompBAM_1.17.0.tar.gz |
| Windows Binary (x86_64) | ompBAM_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | ompBAM_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | ompBAM_1.17.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ompBAM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ompBAM |
| Bioc Package Browser | https://code.bioconductor.org/browse/ompBAM/ |
| Package Short Url | https://bioconductor.org/packages/ompBAM/ |
| Package Downloads Report | Download Stats |